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- PDB-8yra: The Cyro-EM Structure of human SLC26A3 with specific inhibitor DR... -

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Basic information

Entry
Database: PDB / ID: 8yra
TitleThe Cyro-EM Structure of human SLC26A3 with specific inhibitor DRAinh-A250
ComponentsChloride anion exchanger
KeywordsMEMBRANE PROTEIN / Chloride anion exchanger
Function / homology
Function and homology information


Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity ...Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / monoatomic anion transport / membrane hyperpolarization / chloride transmembrane transporter activity / sperm capacitation / monoatomic ion transport / sperm midpiece / chloride transmembrane transport / cellular response to cAMP / brush border membrane / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
: / CHOLESTEROL HEMISUCCINATE / Chloride anion exchanger
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsFeng, J.R. / Dang, S.
Funding support Hong Kong, 5items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)GRF16103321 Hong Kong
The University Grants Committee, Research Grants Council (RGC)GRF16102822 Hong Kong
The University Grants Committee, Research Grants Council (RGC)GRF16100223 Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6001-21EF Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6012-22GF Hong Kong
CitationJournal: To Be Published
Title: Structural Insights into the Inhibition Mechanism of Human DRA
Authors: Feng, J.R. / Dang, S.
History
DepositionMar 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloride anion exchanger
B: Chloride anion exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,91112
Polymers169,1832
Non-polymers4,72810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Chloride anion exchanger / Down-regulated in adenoma / Protein DRA / Solute carrier family 26 member 3


Mass: 84591.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A3, DRA / Production host: Homo sapiens (human) / References: UniProt: P40879
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1LZR / 2-[7-[(3-bromophenyl)methoxy]-4,8-dimethyl-2-oxidanylidene-chromen-3-yl]ethanoic acid


Mass: 417.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H17BrO5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The Cyo-EM structure of human SLC26A3 transporter with inhibitor DRAinh-A250
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0845 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 25 mM Tris-HCl,150 mM NaCl,0.005% GDN
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
225 mMTris(hydroxymethyl)aminomethaneTris-HCl1
30.005 %glyco-diosgeninGDN1
450 uMDRAinh-A250DRAinh-A2501
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: blot with filter paper for 3-4 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 50.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2452
Details: Images were collected in movie-mode containing 40 frames.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1Gautomatchv0.56particle selection
2EPU2.10.0image acquisition
4Gctfv1.18CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11cryoSPARCv3.0.1initial Euler assignment
12cryoSPARCv2.15.0initial Euler assignment
13cryoSPARCv3.0.1final Euler assignment
14cryoSPARCv2.15.0final Euler assignment
16cryoSPARCv3.0.13D reconstruction
17cryoSPARCv2.15.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218752 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingAccession code: AF-P40879 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311570
ELECTRON MICROSCOPYf_angle_d0.5615752
ELECTRON MICROSCOPYf_dihedral_angle_d7.6471610
ELECTRON MICROSCOPYf_chiral_restr0.0411876
ELECTRON MICROSCOPYf_plane_restr0.0031918

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